What is the genome size of each bin?

Question

[MEITUO]

Hi

Does anyone know the genome size of each bin?

I binning contigs and get bins, so each bins can regard as one genome, but how i can know the genome size.

My thought is in each bins it has many contigs, and I cluster them with cover 95% to get non-redundant contigs set, and then adding all length of contigs in the non-redundant contigs set, and this value is the genome size of each bin.

Is this right?

[lieven.sterck]

sorry to tell , but way too little info in your post to get meaningful (if any at all) replies on it.

what kind of bins are you talking about? related to a tool or software you are using?

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[andres.firrincieli]

You should not remove redundant contigs. By doing so, you could falsify the strain heterogeneity index from CheckM.

Answer 1

[Mensur Dlakic]

The answer is that you can't be sure of the genome size with certainty. But yes, the sum of contigs is indicative of genome size, especially if you confirm that a bin has a genome that is mostly complete and not terribly contaminated. A tool like CheckM can provide that information.

I don't think you need to remove the redundancy in your bins. I recommend higher identity threshold like 99% if you still want to do it.